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- PDB-8qjr: BRG1 bromodomain in complex with VBC via compound 17 -

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Basic information

Entry
Database: PDB / ID: 8qjr
TitleBRG1 bromodomain in complex with VBC via compound 17
Components
  • Elongin-B
  • Elongin-C
  • Transcription activator BRG1
  • von Hippel-Lindau disease tumor suppressor
KeywordsGENE REGULATION / BRG1 / BROMODOMAIN / VHL / ELONGIN / VBC / E3 LIGASE / VON HIPPEL-LINDAU / UBIQUITINASE
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / regulation of cellular response to hypoxia / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity ...positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / regulation of cellular response to hypoxia / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / transcription elongation factor activity / target-directed miRNA degradation / RNA polymerase I preinitiation complex assembly / elongin complex / RSC-type complex / ATP-dependent chromatin remodeler activity / regulation of nucleotide-excision repair / host-mediated activation of viral transcription / Replication of the SARS-CoV-1 genome / nucleosome disassembly / VCB complex / Cul5-RING ubiquitin ligase complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Cul2-RING ubiquitin ligase complex / positive regulation of T cell differentiation / intracellular membraneless organelle / nuclear androgen receptor binding / positive regulation of double-strand break repair / SUMOylation of ubiquitinylation proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of signal transduction by p53 class mediator / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Chromatin modifying enzymes / Formation of RNA Pol II elongation complex / DNA polymerase binding / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / transcription coregulator binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Formation of the beta-catenin:TCF transactivating complex / helicase activity / negative regulation of cell growth / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / kinetochore / positive regulation of miRNA transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of expression of SLITs and ROBOs / RMTs methylate histone arginines / nuclear matrix / fibrillar center / cell morphogenesis / ubiquitin-protein transferase activity / p53 binding / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / positive regulation of cold-induced thermogenesis / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex ...SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SKP1/BTB/POZ domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Chem-VLH / von Hippel-Lindau disease tumor suppressor / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsKerry, P.S. / Hole, A.J. / Perez-Dorado, J.I.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2024
Title: PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models.
Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / ...Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / Gordon, D. / Hamman, B.D. / Harbin, A. / Haskell, R. / He, M. / Hole, A.J. / Januario, T. / Kerry, P.S. / Koenig, S.G. / Li, L. / Merchant, M. / Perez-Dorado, I. / Pizzano, J. / Quinn, C. / Rose, C.M. / Rousseau, E. / Soto, L. / Staben, L.R. / Sun, H. / Tian, Q. / Wang, J. / Wang, W. / Ye, C.S. / Ye, X. / Zhang, P. / Zhou, Y. / Yauch, R. / Dragovich, P.S.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Transcription activator BRG1
H: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,24019
Polymers111,3128
Non-polymers2,92911
Water1,02757
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
G: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29111
Polymers55,6564
Non-polymers1,6357
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
H: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9498
Polymers55,6564
Non-polymers1,2944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.68, 88.044, 84.978
Angle α, β, γ (deg.)90, 105.89, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 8 molecules ADBECFGH

#1: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18702.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#4: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 14230.447 Da / Num. of mol.: 2 / Fragment: UNP residues 1418-1536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Non-polymers , 5 types, 68 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-VLH / (2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]pyridin-2-yl]oxycyclobutyl]oxypiperidin-1-yl]ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 1068.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C57H69N11O8S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 27 mM HEPES pH 6.8, 73 mM HEPES pH 8.6, 1.0 M NaI

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→80.64 Å / Num. obs: 20137 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.3
Reflection shellResolution: 3.17→3.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2 / Num. unique obs: 3675 / CC1/2: 0.755 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→80.64 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.523
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 966 -RANDOM
Rwork0.262 ---
obs0.2628 20137 98.8 %-
Displacement parametersBiso mean: 67.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.4345 Å20 Å2-12.8328 Å2
2--2.7539 Å20 Å2
3----5.1884 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3.17→80.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7290 0 196 57 7543
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0057656HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7510370HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2769SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1262HARMONIC5
X-RAY DIFFRACTIONt_it7656HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion976SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6033SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion16.17
LS refinement shellResolution: 3.17→3.19 Å
RfactorNum. reflection% reflection
Rfree0.374 16 -
Rwork0.3189 --
obs0.3207 420 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.43521.2377-1.04241.8365-0.7892.2724-0.0968-0.23790.1358-0.2379-0.11170.63810.13580.63810.2085-0.00320.02190.0699-0.05460.0657-0.194169.7562-7.961727.814
27.79951.7538-2.13575.8167-2.00293.0072-0.1392-0.35-0.3125-0.35-0.09620.1988-0.31250.19880.2355-0.14480.0477-0.0591-0.1928-0.0085-0.065953.7133-1.124222.9995
31.6744-0.38130.14711.9148-0.26351.5016-0.017-0.2705-0.0937-0.27050.022-0.09-0.0937-0.09-0.0050.0051-0.02490.0546-0.18830.0248-0.048133.3895-17.678813.2558
44.7880.229-3.40951.24340.09235.9226-0.0621-0.4941-0.0441-0.49410.0524-0.724-0.0441-0.7240.0098-0.109-0.0359-0.06030.0829-0.0861-0.164332.5078-3.3705-38.4375
56.2253-3.046-3.29017.82922.71124.9265-0.23710.03050.61950.0305-0.1908-0.39270.6195-0.39270.42790.0169-0.07080.0963-0.19080.0091-0.16528.6051-9.9265-22.0496
61.1925-0.10740.07063.19820.67433.08610.11290.29110.02780.2911-0.0878-0.38340.0278-0.3834-0.0252-0.0730.01180.0771-0.1380.0166-0.10126.13126.86970.3594
73.26260.0601-0.28175.086-1.14966.5887-0.21880.1578-0.22320.15780.1865-0.0102-0.2232-0.01020.0324-0.00840.1090.0458-0.3012-0.0763-0.077113.5842-56.02255.0354
811.11332.5306-0.23687.6354-1.68556.2088-0.2237-0.32590.2342-0.32590.9146-0.840.2342-0.84-0.69090.0983-0.13560.0036-0.15230.27750.033124.072644.450624.2194
9-0.1238-0.08570.19990.85530.04320.1238-0.0180.01760.00470.01760.0824-0.06210.0047-0.0621-0.0645-0.0408-0.01940.1029-0.35340.0172-0.085725.6193-5.40959.1501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|103 }A1 - 103
2X-RAY DIFFRACTION2{ B|16 - B|112 }B16 - 112
3X-RAY DIFFRACTION3{ C|61 - C|213 }C61 - 213
4X-RAY DIFFRACTION4{ D|1 - D|103 }D1 - 103
5X-RAY DIFFRACTION5{ E|16 - E|112 }E16 - 112
6X-RAY DIFFRACTION6{ F|60 - F|213 }F60 - 213
7X-RAY DIFFRACTION7{ G|1457 - G|1566 }G1457 - 1566
8X-RAY DIFFRACTION8{ H|1457 - H|1559 }H1457 - 1559
9X-RAY DIFFRACTION9{ C|305 - C|305 F|303 - F|303 }C305
10X-RAY DIFFRACTION9{ C|305 - C|305 F|303 - F|303 }F303

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